Variant report

Variant	rs2396373
Chromosome Location	chr6:44983134-44983135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44974489..44977160-chr6:44980461..44983338,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1041333	0.86[EUR][1000 genomes]
rs10948186	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs10948187	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs10948190	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10948194	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10948195	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12191518	0.84[EUR][1000 genomes]
rs1293598	0.80[EUR][1000 genomes]
rs1329716	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs1360196	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1555681	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1576382	0.87[EUR][1000 genomes]
rs1854547	0.86[EUR][1000 genomes]
rs1980265	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2396370	0.87[EUR][1000 genomes]
rs2396371	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs3778507	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs3799967	0.86[CEU][hapmap]
rs3799968	0.85[CEU][hapmap]
rs3799971	0.85[CEU][hapmap]
rs3799978	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3846896	0.81[EUR][1000 genomes]
rs494982	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs57020561	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs636845	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs6458415	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs6903576	0.82[EUR][1000 genomes]
rs6904015	0.86[CEU][hapmap]
rs6910294	0.89[CEU][hapmap]
rs6919485	0.85[EUR][1000 genomes]
rs6923519	0.84[EUR][1000 genomes]
rs9349303	0.93[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9357464	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs9357471	0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs9367211	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs9369514	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs9369515	0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9369516	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9369523	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9381359	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9395049	0.82[CEU][hapmap]
rs9395051	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9395055	0.83[EUR][1000 genomes]
rs9395069	0.87[JPT][hapmap]
rs9463054	0.87[EUR][1000 genomes]
rs9463055	0.88[EUR][1000 genomes]
rs9463078	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9472403	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9472418	0.93[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs976699	0.84[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758051	chr6:44879791-45056758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2759423	chr6:44879791-45056758	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv462938	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv470817	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv603007	chr6:44909515-45008779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	esv2757164	chr6:44953758-44989519	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv603008	chr6:44958372-45081821	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv2762589	chr6:44982992-45044580	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2396373	SUPT3H	cis	multi-tissue	Pritchard
rs2396373	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44964600-44983600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:44965800-44983400	Weak transcription	Primary B cells from cord blood	blood
3	chr6:44966400-44993600	Weak transcription	HepG2	liver
4	chr6:44970800-44988600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:44970800-44989000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:44971400-44988800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:44972000-44983800	Weak transcription	Adipose Nuclei	Adipose
8	chr6:44974800-45004600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:44975000-44983800	Weak transcription	Brain Anterior Caudate	brain
10	chr6:44977200-44988800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:44977600-44993800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:44978600-44988600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:44979000-44983200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:44979000-44983400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:44979000-44983600	Weak transcription	Fetal Brain Male	brain
16	chr6:44979200-44983600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:44979400-44984000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:44980600-44989000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:44980800-44983600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:44981000-44983200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:44981000-44983200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:44981000-44983400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:44981200-44983200	Weak transcription	Brain Angular Gyrus	brain
24	chr6:44981600-44983200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:44981600-44983200	Weak transcription	Fetal Intestine Large	intestine
26	chr6:44981600-44983400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:44981600-44983800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:44981600-44994800	Weak transcription	Aorta	Aorta
29	chr6:44981600-44994800	Weak transcription	Pancreas	Pancrea
30	chr6:44981800-44983400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:44981800-44988200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:44981800-44988800	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:44982200-44983800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:44982200-44987200	Weak transcription	Dnd41	blood
35	chr6:44982600-44984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:44982600-44989000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:44983000-44984600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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